SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data


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Documentation for package ‘SpidermiR’ version 1.7.4

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SpidermiR-package Download data
Case_Study1_loading_1_network Loading 1 network of shared protein domanin
Case_Study1_loading_2_network Loading 2 network of shared protein domanin
Case_Study1_loading_3_network Loading 3 network of shared protein domanin
Case_Study1_loading_4_network Loading 4 network of shared protein domanin
Case_Study2_loading_1_network Loading 1 network of Protein Interactions (PI)
Case_Study2_loading_2_network Loading 2 network of Protein Interactions (PI) with miRNAs
Case_Study2_loading_3_network Loading 3 network of Protein Interactions (PI) with miRNAs
SpidermiR Download data
SpidermiRanalyze_Community_detection Find community detection
SpidermiRanalyze_Community_detection_bi Community detection from biomarkers of interest
SpidermiRanalyze_Community_detection_net Find the network of community detection and direct biormarker
SpidermiRanalyze_degree_centrality Ranking degree centrality genes
SpidermiRanalyze_DEnetworkTCGA Integration with TCGA data in order to obtain a network of differentially expressed (DE) genes or miRNAs.
SpidermiRanalyze_direct_net Searching by biomarkers of interest with direct interaction
SpidermiRanalyze_direct_subnetwork Searching by biomarkers of interest with direct interaction by ONLY the nodes in BI
SpidermiRanalyze_mirnanet_pharm Integration of pharmacomiR in the network
SpidermiRanalyze_mirna_gene_complnet Integration of microRNA target gene networks.
SpidermiRanalyze_mirna_network Integration of microRNA target networks.
SpidermiRanalyze_subnetwork_neigh Searching by biomarkers of interest and all the edges among this bunch of nodes
SpidermiRdownload_miRNAextra_cir Download miRNA validated database
SpidermiRdownload_miRNALNC_miRNA Download microRNAs binding sites on long non coding RNA from lncRNome database
SpidermiRdownload_miRNALNC_RNA Download Long Non-Coding RNA (LNC-RNA) from lncRNome database
SpidermiRdownload_miRNAprediction Download miRNA predicted database
SpidermiRdownload_miRNAvalidate Download miRNA validated database
SpidermiRdownload_net Download the network from GeneMania.
SpidermiRdownload_pharmacomir Download both miRNA target and the gene-drug interaction from PharmacomiR database
SpidermiRprepare_NET Prepare matrix of gene network from Genamania with Ensembl Gene ID, and gene symbols
SpidermiRquery_disease Visualize disease categories
SpidermiRquery_networks_type Network categories
SpidermiRquery_species Searching by network species
SpidermiRquery_spec_networks Searching by network categories
SpidermiRvisualize_3Dbarplot plots the 3D barplot
SpidermiRvisualize_adj_matrix plots the adjacency matrix of the network
SpidermiRvisualize_BI Visualize results obtained by SpidermiR analysis starting form a set of biomarker of interest
SpidermiRvisualize_degree_dist plots the degree distribution of the network
SpidermiRvisualize_direction Visualize results obtained by SpidermiR analysis with the direction of the interaction (pharmaco-gene and miRNA-gene)
SpidermiRvisualize_mirnanet Visualize results obtained by SpidermiR analysis
SpidermiRvisualize_plot_target Visualize results obtained by SpidermiRanalyze_mirna_network